You may want to check under "Job Assignment" and look at the properties for the entities you selected. The "Zmin" and resultant "D" (depth) control depths for each individual hole.
I believe the "Bottom Level" parameter controls only the maximum depth that can be machined to.
Another item of interest in "Job Assignment/properties" is the "Drill tip compensation". It will allow the drill to penetrate the part further so the entire hole is to the full diameter rather than just the tip of the drill breaking through. It is based on the drill point angle.